High rate of calculation errors in mismatch distribution analysis results in numerous false inferences of biological importance

AbstractQuaternary environmental changes fundamentally influenced the genetic diversity of temperate-zone terrestrial animals, including those in the Japanese Archipelago. The genetic diversity of present-day populations is taxon- and region-specific, but its determinants are poorly understood. Here, we analyzed cytochrome b gene (Cytb) sequences (1140 bp) of mitochondrial DNA (mtDNA) to elucidate the factors determining the genetic variation in three species of large moles: Mogera imaizumii and Mogera wogura, which occur in central and southern mainland Japan (Honshu, Shikoku, and Kyushu), and Mogera robusta, which occurs on the nearby Asian continent. Network construction with the Cytb sequences revealed 10 star-shaped clusters with apparent geographic affinity. Mismatch distribution analysis showed that modes of pairwise nucleotide differences (τ values) were grouped into five classes in terms of the level, implying the occurrence of five stages for rapid expansion. It is conceivable that severe cold periods and subsequent warm periods during the late Quaternary were responsible for the population expansion events. The first and third oldest events included island-derived haplotypes, indicative of the involvement of land bridge formation between remote islands, hence suggesting an association of the ends of the penultimate (PGM, ca. 130,000 years ago) and last (LGM, ca. 15,000 years ago) glacial maxima, respectively. Since the third event was followed by the fourth, it is plausible that the termination of the Younger Dryas and subsequent abrupt warming ca. 11,500 years ago facilitated the fourth expansion event. The second event most likely corresponded to early marine isotope stage (MIS) 3 (ca. 53,000 years ago) when the glaciation and subsequent warming period were predicted to have influenced biodiversity. Utilization of the critical times of 130,000, 53,000, 15,000, and 11,500 years ago as calibration points yielded evolutionary rates of 0.03, 0.045, 0.10 and 0.10 substitutions/site/million years, respectively, showing a time-dependent manner whose pattern was similar to that seen in small rodents reported in our previous studies. The age of the fifth expansion event was calculated to be 5800 years ago with a rate of 0.10 substitutions/site/million years ago during the mid-Holocene, suggestive of the influence of humans or other unspecified reasons, such as the Jomon marine transgression.

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Patterns of Genetic Variation in the Eisenia nordenskioldi Complex (Oligochaeta: Lumbricidae) along an Elevation Gradient in Northern China

Diversity ◽

10.3390/d14010035 ◽

2022 ◽

Vol 14 (1) ◽

pp. 35

Author(s):

Yufeng Zhang ◽

Yiming Zhang ◽

Hui Wu ◽

Congsheng Li ◽

Nonillon M. Aspe ◽

...

Keyword(s):

Genetic Diversity ◽

Elevation Gradient ◽

Northern China ◽

External Morphology ◽

Distribution Analysis ◽

Limited Sample ◽

Southern Limit ◽

Earthworm Species ◽

Mismatch Distribution Analysis ◽

Eisenia Nordenskioldi

Eisenia nordenskioldi is the dominant earthworm species in many tundra and boreal habitats. Nothing is known about the genetic diversity of this species along the elevation gradient in China. This study sampled 28 individuals in the E. nordenskioldi complex from Wuling Mountain, northern China, to examine their external morphology and genetic diversity. Mt. Wuling is the southern limit of the distribution of the E. nordenskioldi complex. The specimens from Mt. Wuling were classified into three groups along an elevation gradient. Mismatch distribution analysis suggested that the Pleistocene glaciations possibly did not significantly affect the distribution of earthworm species in this region. We also found that elevation affected the genetic diversity, but not the external morphology of E. nordenskioldi. Given the altitudinal genetic diversity within the E. nordenskioldi complex, the phylogeography of this species provides important information for the zoogeographic reconstruction of the mountains in northern China. With the relatively limited sample size, the result is not conclusive, and further studies need to be conducted in the future to verify the results.

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Statistical analysis to characterize transport of nutrients in groundwater near an abandoned feedlot

Hydrology and Earth System Sciences ◽

10.5194/hess-17-4897-2013 ◽

2013 ◽

Vol 17 (12) ◽

pp. 4897-4906 ◽

Cited By ~ 6

Author(s):

P. Gbolo ◽

P. Gerla

Keyword(s):

Multivariate Analyses ◽

Nitrate Nitrogen ◽

Chemical Species ◽

Ammonium Nitrogen ◽

High Rate ◽

Total Carbon ◽

Distribution Analysis ◽

Groundwater Samples ◽

Dissolved Reactive Phosphorus ◽

Reactive Phosphorus

Abstract. Surface water from a lagoon and groundwater samples from 17 wells within and near an abandoned feedlot in northwestern Minnesota, USA, were analyzed for carbon, nutrients, and field parameters. The feedlot is surrounded by wetlands that act as receptors of nutrients from the feedlot. Q- and R-mode multivariate analyses performed on total carbon (TC), inorganic carbon (IC), total organic carbon (TOC), nitrite-nitrogen (NO2-N), nitrate-nitrogen (NO3-N), ammonium-nitrogen (NH4-N), soluble or dissolved reactive phosphorus (DRP), and total phosphorus (TP) indicated three groups of the chemical species, which reflected variability in groundwater chemistry. Factor analysis indicated approximately 82% of the variability in factor 1 was caused by TC, IC, TOC, and DRP, while in factor 2 approximately 79% of the variability was caused by NO2-N, NO3-N, and TP. In factor 3, only NH4-N contributed 31% of the variability. Groundwater isotope and spatial distribution analysis indicated reduced nitrate concentration from the source to the wetlands, with variation in NO2-N, NO3-N, and NH4-N concentrations attributed to the plant nutrient uptake, high rate of denitrification and/or the dissimilatory nitrate reduction to ammonium. This study indicated the value of multivariate analyses in characterizing variability in groundwater quality.

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Demographic history of Trinorchestia longiramus (Amphipoda, Talitridae) in South Korea inferred from mitochondrial DNA sequence variation

Crustaceana ◽

10.1163/15685403-00003608 ◽

2016 ◽

Vol 89 (13) ◽

pp. 1559-1573 ◽

Cited By ~ 2

Author(s):

Jiyoung Woo ◽

Hyesuck An ◽

Byung-Jin Lim ◽

Ha Yeun Song ◽

Min-Seop Kim ◽

...

Keyword(s):

Demographic History ◽

Haplotype Diversity ◽

Nucleotide Sequence Analysis ◽

Distribution Analysis ◽

Demographic Bottleneck ◽

Dna Sequence Variation ◽

Mismatch Distribution Analysis ◽

History Of ◽

Amova Analysis ◽

Mitochondrial Cytochrome Oxidase

We investigated the demographic history ofTrinorchestia longiramusJo, 1988 using the nucleotide sequence analysis of the mitochondrial cytochrome oxidase subunit I (COI) gene from 277 individuals collected from eight Korean populations. From the low haplotype diversity and nucleotide diversity in all populations, a neutrality test, and mismatch distribution analysis, the species appears to have recently experienced a prolonged or severe demographic bottleneck. Pairwise populationFSTestimates and AMOVA [= Analysis of Molecular Variance] results showed that substantial differentiation is present between the southern and eastern populations. The population structure ofT. longiramusmay have been influenced by glacial population extinctions and interglacial colonization during the Pleistocene ice-ages.

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pgHMA: Application of the Heteroduplex Mobility Assay Analysis in Phylogenetics and Population Genetics

10.22541/au.162729410.03237560/v1 ◽

2021 ◽

Author(s):

Teng Li ◽

Thomas Wong ◽

Louis Ranjard ◽

Allen Rodrigo

Keyword(s):

Population Genetics ◽

Mismatch Distribution ◽

Phylogenetic Trees ◽

Nucleotide Sequences ◽

Bootstrap Support ◽

Distribution Analysis ◽

Sequencing Data ◽

Effective Population ◽

Heteroduplex Mobility Assay ◽

Mismatch Distributions

The Heteroduplex mobility assay (HMA) has proven to be a robust tool for the detection of genetic variation. Here, we describe a simple and rapid application of the HMA by microfluidic capillary electrophoresis, for phylogenetics and population genetic analyses (pgHMA). We show how commonly applied techniques in phylogenetics and population genetics have equivalents with pgHMA: phylogenetic reconstruction with bootstrapping, skyline plots, and mismatch distribution analysis. We assess the performance and accuracy of pgHMA by comparing the results obtained against those obtained using standard methods of analyses applied to sequencing data. The resulting comparisons demonstrate that: (1) there is a significant linear relationship (R = 0.992) between heteroduplex mobility and genetic distance; (2) phylogenetic trees obtained by HMA and nucleotide sequences present nearly identical topologies; (3) clades with high pgHMA parametric bootstrap support also have high bootstrap support on nucleotide phylogenies; (4) skyline plots estimated from the UPGMA trees of HMA and Bayesian trees of nucleotide data reveal similar trends, especially for the median trend estimate of effective population size; and (5) optimized mismatch distributions of HMA are closely fitted to the mismatch distributions of nucleotide sequences. In summary, pgHMA is an easily-applied method for approximating phylogenetic diversity and population trends. KEYWORDS: bootstrap, heteroduplex mobility assay, mismatch distribution, phylogenetics, skyline plot

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Intraspecific divergences and phylogeography of Panzerina lanata (Lamiaceae) in northwest China

PeerJ ◽

10.7717/peerj.6264 ◽

2019 ◽

Vol 7 ◽

pp. e6264 ◽

Cited By ~ 3

Author(s):

Yanfen Zhao ◽

Hongxiang Zhang ◽

Borong Pan ◽

Mingli Zhang

Keyword(s):

Genetic Differentiation ◽

Northwest China ◽

Intraspecific Diversity ◽

Distribution Analysis ◽

Climatic Fluctuations ◽

Intraspecific Divergence ◽

Intergenic Spacers ◽

Helan Mountains ◽

Mismatch Distribution Analysis ◽

The Impact

Climatic fluctuations during the Quaternary significantly affect many species in their intraspecific divergence and population structure across northwest China. In order to investigate the impact of climate change on herbaceous plants, we studied Panzerina lanata (Lamiaceae), a widely distributed species. Sequences of two chloroplast DNA (cpDNA) intergenic spacers (trnH-psbA and rpoB-trnC) and a nuclear ribosomal region (nrDNA, ITS) were generated from 27 populations of Panzerina lanata and resulted in the identification of seven chloroplast haplotypes and thirty-two nuclear haplotypes. We applied AMOVA, neutrality test and mismatch distribution analysis to estimate genetic differentiation and demographic characteristics. The divergence times of the seven cpDNA haplotypes were estimated using BEAST. Our results revealed high levels of genetic diversity (cpDNA: Hcp = 0.6691, HT = 0.673; nrDNA: Hnr = 0.5668, HT = 0.577). High level of genetic differentiation (GST = 0.950) among populations was observed in the cpDNA sequences, while the genetic differentiation values (GST = 0.348) were low in nuclear sequences. AMOVA results revealed major genetic variation among the three groups: northern, central, and eastern group. However, the genetic differentiation in ITS data was not found. The species distribution modeling and demographic analysis indicated that P. lanata had not experienced recent range expansion. The occurrence of divergence between seven cpDNA haplotypes, probably during Pleistocene, coincides with aridification and expansion of the desert across northwest China that resulted in species diversification and habitat fragmentation. In addition, we discovered that the deserts and the Helan Mountains acted as effective geographic barriers that promoting the intraspecific diversity of P. lanata.

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A New System For Optomanual Semiautomatic Quantitative Image Analysis

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100078596 ◽

1977 ◽

Vol 35 ◽

pp. 210-211

Author(s):

H.P. Rohr

Keyword(s):

Image Analysis ◽

Volume Density ◽

List Type ◽

Distribution Analysis ◽

Type Number ◽

Point Counting ◽

Human Eye ◽

Quantitative Image ◽

Point Density ◽

Electronic Counting

Today, in image analysis the broadest possible rationalization and economization have become desirable. Basically, there are two approaches for image analysis: The image analysis through the so-called scanning methods which are usually performed without the human eye and the systems of optical semiautomatic analysis completely relying on the human eye.The new MOP AM 01 opto-manual system (fig.) represents one of the very promising approaches in this field. The instrument consists of an electronic counting and storing unit, which incorporates a microprocessor and a keyboard for choice of measuring parameters, well designed for easy use.Using the MOP AM 01 there are three possibilities of image analysis:the manual point counting,the opto-manual point counting andthe measurement of absolute areas and/or length (size distribution analysis included).To determine a point density for the calculation of the corresponding volume density the intercepts lying within the structure are scanned with the light pen.

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Structure of Palladium Single-Crystal Films Prepared by Flash Evaporation onto (001) NaCl Substrates

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100069272 ◽

1970 ◽

Vol 28 ◽

pp. 456-457

Author(s):

L. E. Murr ◽

G. Wong

Keyword(s):

Single Crystal ◽

High Vacuum ◽

Ultra High Vacuum ◽

High Rate ◽

Flash Evaporation ◽

Optimum Load ◽

Single Crystal Films ◽

Crystal Films ◽

A Current

Palladium single-crystal films have been prepared by Matthews in ultra-high vacuum by evaporation onto (001) NaCl substrates cleaved in-situ, and maintained at ∼ 350° C. Murr has also produced large-grained and single-crystal Pd films by high-rate evaporation onto (001) NaCl air-cleaved substrates at 350°C. In the present work, very large (∼ 3cm2), continuous single-crystal films of Pd have been prepared by flash evaporation onto air-cleaved (001) NaCl substrates at temperatures at or below 250°C. Evaporation rates estimated to be ≧ 2000 Å/sec, were obtained by effectively short-circuiting 1 mil tungsten evaporation boats in a self-regulating system which maintained an optimum load current of approximately 90 amperes; corresponding to a current density through the boat of ∼ 4 × 104 amperes/cm2.

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Local atomic structure of relaxor ferroelectric solids studied by pulsed neutron scattering

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100170505 ◽

1994 ◽

Vol 52 ◽

pp. 554-555

Author(s):

T. Egami ◽

H. D. Rosenfeld ◽

S. Teslic

Keyword(s):

Neutron Scattering ◽

Atomic Structure ◽

Argonne National Laboratory ◽

Relaxor Ferroelectrics ◽

Relaxor Ferroelectric ◽

Crystallographic Structure ◽

Chemical Inhomogeneity ◽

Distribution Analysis ◽

Ferroelectric Transition ◽

Pulsed Neutron

Relaxor ferroelectrics, such as Pb(Mg1/3Nb2/3)O3 (PMN) or (Pb·88La ·12)(Zr·65Ti·35)O3 (PLZT), show diffuse ferroelectric transition which depends upon frequency of the a.c. field. In spite of their wide use in various applications details of their atomic structure and the mechanism of relaxor ferroelectric transition are not sufficiently understood. While their crystallographic structure is cubic perovskite, ABO3, their thermal factors (apparent amplitude of thermal vibration) is quite large, suggesting local displacive disorder due to heterovalent ion mixing. Electron microscopy suggests nano-scale structural as well as chemical inhomogeneity.We have studied the atomic structure of these solids by pulsed neutron scattering using the atomic pair-distribution analysis. The measurements were made at the Intense Pulsed Neutron Source (IPNS) of Argonne National Laboratory. Pulsed neutrons are produced by a pulsed proton beam accelerated to 750 MeV hitting a uranium target at a rate of 30 Hz. Even after moderation by a liquid methane moderator high flux of epithermal neutrons with energies ranging up to few eV’s remain.

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